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Tayeh N, Hofer JMI, Aubert G, Jacquin F, Turner L, Kreplak J, Paajanen P, Le Signor C, Dalmais M, Pflieger S, Geffroy V, Ellis N, Burstin J. afila, the origin and nature of a major innovation in the history of pea breeding. THE NEW PHYTOLOGIST 2024; 243:1247-1261. [PMID: 38837425 DOI: 10.1111/nph.19800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 03/22/2024] [Indexed: 06/07/2024]
Abstract
The afila (af) mutation causes the replacement of leaflets by a branched mass of tendrils in the compound leaves of pea - Pisum sativum L. This mutation was first described in 1953, and several reports of spontaneous af mutations and induced mutants with a similar phenotype exist. Despite widespread introgression into breeding material, the nature of af and the origin of the alleles used remain unknown. Here, we combine comparative genomics with reverse genetic approaches to elucidate the genetic determinants of af. We also investigate haplotype diversity using a set of AfAf and afaf cultivars and breeding lines and molecular markers linked to seven consecutive genes. Our results show that deletion of two tandemly arranged genes encoding Q-type Cys(2)His(2) zinc finger transcription factors, PsPALM1a and PsPALM1b, is responsible for the af phenotype in pea. Eight haplotypes were identified in the af-harbouring genomic region on chromosome 2. These haplotypes differ in the size of the deletion, covering more or less genes. Diversity at the af locus is valuable for crop improvement and sheds light on the history of pea breeding for improved standing ability. The results will be used to understand the function of PsPALM1a/b and to transfer the knowledge for innovation in related crops.
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Affiliation(s)
- Nadim Tayeh
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Julie M I Hofer
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Grégoire Aubert
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Françoise Jacquin
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Lynda Turner
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Jonathan Kreplak
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Pirita Paajanen
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Christine Le Signor
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
| | - Marion Dalmais
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, 91190, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, 91190, France
| | - Stéphanie Pflieger
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, 91190, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, 91190, France
| | - Valérie Geffroy
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, 91190, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, 91190, France
| | - Noel Ellis
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Judith Burstin
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, F-21000, France
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2
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Deng D, Sun S, Wu W, Duan C, Wu X, Zhu Z. Fine mapping and identification of a Fusarium wilt resistance gene FwS1 in pea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:171. [PMID: 38918246 DOI: 10.1007/s00122-024-04682-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/20/2024] [Indexed: 06/27/2024]
Abstract
KEY MESSAGE A Fusarium wilt resistance gene FwS1 on pea chromosome 6 was identified and mapped to a 91.4 kb region by a comprehensive genomic-based approach, and the gene Psat6g003960 harboring NB-ARC domain was identified as the putative candidate gene. Pea Fusarium wilt, incited by Fusarium oxysporum f. sp. pisi (Fop), has always been a devastating disease that causes severe yield losses and economic damage in pea-growing regions worldwide. The utilization of pea cultivars carrying resistance gene is the most efficient approach for managing this disease. In order to finely map resistance gene, F2 populations were established through the cross between Shijiadacaiwan 1 (resistant) and Y4 (susceptible). The resistance genetic analysis indicated that the Fop resistance in Shijiadacaiwan 1 was governed by a single dominant gene, named FwS1. Based on the bulked segregant analysis sequencing analyses, the gene FwS1 was initially detected on chromosome 6 (i.e., linking group II, chr6LG2), and subsequent linkage mapping with 589 F2 individuals fine-mapped the gene FwS1 into a 91.4 kb region. The further functional annotation and haplotype analysis confirmed that the gene Psat6g003960, characterized by a NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) domain, was considered as the most promising candidate gene. The encoding amino acids were altered by a "T/C" single-nucleotide polymorphism (SNP) in the first exon of the Psat6g003960, and based on this SNP locus, the molecular marker A016180 was determined to be a diagnostic marker for FwS1 by validating its specificity in both pea accessions and genetic populations with different genetic backgrounds. The FwS1 with diagnostic KASP marker A016180 could facilitate marker-assisted selection in resistance pea breeding in pea. In addition, a comparison of the candidate gene Psat6g003960 in 74SN3B and SJ1 revealed the same sequences. This finding indicated that 74SN3B carried the candidate gene for FwS1, suggesting that FwS1 and Fwf may be closely linked or an identical resistant gene against Fusarium wilt.
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Affiliation(s)
- Dong Deng
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Suli Sun
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenqi Wu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Canxing Duan
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xuehong Wu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
| | - Zhendong Zhu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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3
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Caudal É, Loegler V, Dutreux F, Vakirlis N, Teyssonnière É, Caradec C, Friedrich A, Hou J, Schacherer J. Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast. Nat Genet 2024; 56:1278-1287. [PMID: 38778243 PMCID: PMC11176082 DOI: 10.1038/s41588-024-01769-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Gene expression is an essential step in the translation of genotypes into phenotypes. However, little is known about the transcriptome architecture and the underlying genetic effects at the species level. Here we generated and analyzed the pan-transcriptome of ~1,000 yeast natural isolates across 4,977 core and 1,468 accessory genes. We found that the accessory genome is an underappreciated driver of transcriptome divergence. Global gene expression patterns combined with population structure showed that variation in heritable expression mainly lies within subpopulation-specific signatures, for which accessory genes are overrepresented. Genome-wide association analyses consistently highlighted that accessory genes are associated with proportionally more variants with larger effect sizes, illustrating the critical role of the accessory genome on the transcriptional landscape within and between populations.
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Affiliation(s)
- Élodie Caudal
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France
| | - Victor Loegler
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France
| | - Fabien Dutreux
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France
| | | | | | - Claudia Caradec
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France
| | - Jing Hou
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France.
| | - Joseph Schacherer
- Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France.
- Institut Universitaire de France (IUF), Paris, France.
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4
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Garg V, Barmukh R, Chitikineni A, Roorkiwal M, Ojiewo C, Bohra A, Thudi M, Singh VK, Kudapa H, Saxena RK, Fountain J, Mir RR, Bharadwaj C, Chen X, Xin L, Pandey MK. Celebrating Professor Rajeev K. Varshney's transformative research odyssey from genomics to the field on his induction as Fellow of the Royal Society. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1504-1515. [PMID: 38206288 PMCID: PMC11123405 DOI: 10.1111/pbi.14282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/17/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024]
Abstract
Professor Rajeev K. Varshney's transformative impact on crop genomics, genetics, and agriculture is the result of his passion, dedication, and unyielding commitment to harnessing the potential of genomics to address the most pressing challenges faced by the global agricultural community. Starting from a small town in India and reaching the global stage, Professor Varshney's academic and professional trajectory has inspired many scientists active in research today. His ground-breaking work, especially his effort to list orphan tropical crops to genomic resource-rich entities, has been transformative. Beyond his scientific achievements, Professor Varshney is recognized by his colleagues as an exemplary mentor, fostering the growth of future researchers, building institutional capacity, and strengthening scientific capability. His focus on translational genomics and strengthening seed system in developing countries for the improvement of agriculture has made a tangible impact on farmers' lives. His skills have been best utilized in roles at leading research centres where he has applied his expertise to deliver a new vision for crop improvement. These efforts have now been recognized by the Royal Society with the award of the Fellowship (FRS). As we mark this significant milestone in his career, we not only celebrate Professor Varshney's accomplishments but also his wider contributions that continue to transform the agricultural landscape.
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Affiliation(s)
- Vanika Garg
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Rutwik Barmukh
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Annapurna Chitikineni
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Manish Roorkiwal
- Khalifa Center for Genetic Engineering and BiotechnologyUnited Arab Emirates UniversityAl AinUAE
| | - Chris Ojiewo
- International Maize and Wheat Improvement Center (CIMMYT)NairobiKenya
| | - Abhishek Bohra
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | | | - Vikas K. Singh
- International Rice Research Institute (IRRI)‐South‐Asia HubInternational Crops Research Institute for the Semi‐Arid TropicsHyderabadIndia
| | - Himabindu Kudapa
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | | | - Jake Fountain
- Department of Plant PathologyUniversity of GeorgiaGriffinGeorgiaUSA
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of AgricultureSKUAST‐KashmirWaduraIndia
| | | | - Xiaoping Chen
- Crops Research InstituteGuangdong Academy of Agricultural Sciences (GDAAS)GuangzhouChina
| | | | - Manish K. Pandey
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
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5
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Li L, Xu JB, Zhu ZW, Ma R, Wu XZ, Geng YK. Genome-wide identification and expression analysis of the SPL transcription factor family and its response to abiotic stress in Pisum sativum L. BMC Genomics 2024; 25:539. [PMID: 38822248 PMCID: PMC11140923 DOI: 10.1186/s12864-024-10262-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/27/2024] [Indexed: 06/02/2024] Open
Abstract
Squamous promoter binding protein-like (SPL) genes encode plant-specific transcription factors (TFs) that play essential roles in modulating plant growth, development, and stress response. Pea (Pisum sativum L.) is a coarse grain crop of great importance in food production, biodiversity conservation and molecular genetic research, providing genetic information and nutritional resources for improving agricultural production and promoting human health. However, only limited researches on the structure and functions of SPL genes exist in pea (PsSPLs). In this study, we identified 22 PsSPLs and conducted a genome-wide analysis of their physical characteristics, chromosome distribution, gene structure, phylogenetic evolution and gene expression patterns. As a result, the PsSPLs were unevenly distributed on the seven chromosomes of pea and harbored the SBP domain, which is composed of approximately 76 amino acid residues. The phylogenetic analysis revealed that the PsSPLs clustered into eight subfamilies and showed high homology with SPL genes in soybean. Further analysis showed the presence of segmental duplications in the PsSPLs. The expression patterns of 22 PsSPLs at different tissues, developmental stages and under various stimulus conditions were evaluated by qRT-PCR method. It was found that the expression patterns of PsSPLs from the same subfamily were similar in different tissues, the transcripts of most PsSPLs reached the maximum peak value at 14 days after anthesis in the pod. Abiotic stresses can cause significantly up-regulated PsSPL19 expression with spatiotemporal specificity, in addition, four plant hormones can cause the up-regulated expression of most PsSPLs including PsSPL19 in a time-dependent manner. Therefore, PsSPL19 could be a key candidate gene for signal transduction during pea growth and development, pod formation, abiotic stress and plant hormone response. Our findings should provide insights for the elucidating of development regulation mechanism and breeding for resistance to abiotic stress pea.
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Affiliation(s)
- Long Li
- Minzu University of China, 100010, Beijing, P.R. China
- College of Agronomy, Hebei Agricultural University, 071001, Baoding, P.R. China
| | - Jian Bo Xu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China
| | - Zhi Wen Zhu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China
| | - Rui Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 712100, Yangling, Shaanxi, P.R. China
| | - Xiao Zong Wu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China.
- Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China.
| | - Yu Ke Geng
- Minzu University of China, 100010, Beijing, P.R. China.
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6
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Brhane H, Hammenhag C. Genetic diversity and population structure analysis of a diverse panel of pea ( Pisum sativum). Front Genet 2024; 15:1396888. [PMID: 38873115 PMCID: PMC11169732 DOI: 10.3389/fgene.2024.1396888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/22/2024] [Indexed: 06/15/2024] Open
Abstract
Breeding resilient cultivars with increased tolerance to environmental stress and enhanced resistance to pests and diseases demands pre-breeding efforts that include understanding genetic diversity. This study aimed to evaluate the genetic diversity and population structure of 265 pea accessions. The diversity arrays technology (DArT) genotyping method was employed to identify single-nucleotide polymorphisms (SNPs) and silico markers. After stringent filtering, 6966 SNP and 8,454 silico markers were selected for diversity analysis. Genetic diversity was estimated by grouping accessions based on plant material type, geographic origin, growth habit, and seed color. Generally, diversity estimations obtained using SNPs were similar to those estimated using silico markers. The polymorphism information content (PIC) of the SNP markers ranged from 0.0 to 0.5, with a quarter of them displaying PIC values exceeding 0.4, making them highly informative. Analysis based on plant material type revealed narrow observed heterozygosity (Ho = 0.02-0.03) and expected heterozygosity (He = 0.26-0.31), with landrace accessions exhibiting the highest diversity. Geographic origin-based diversity analysis revealed Ho = 0.02-0.03 and He = 0.22 to 0.30, with European accessions showing the greatest diversity. Moreover, private alleles unique to landrace (4) and European (22) accessions were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance revealed a highly significant genetic differentiation among accession groups classified by seed color, growth habit, plant material types, and geographic origin (p < 0.01). Principal coordinate analysis and neighbor-joining cluster analysis revealed weak clustering of accessions at different grouping levels. This study underscores the significance of genetic diversity in pea collections, offering valuable insights for targeted breeding and conservation efforts. By leveraging genomic data and exploring untapped genetic resources, pea breeding programs can be fortified to ensure sustainable plant protein production and address future challenges in agriculture.
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Affiliation(s)
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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7
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Yuan Z, Xie X, Liu M, He Y, He L. Mutations of PsPALM1a and PsPALM1b associated with the afila phenotype in Pea. PHYSIOLOGIA PLANTARUM 2024; 176:e14310. [PMID: 38666425 DOI: 10.1111/ppl.14310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 05/01/2024]
Abstract
Semi-leafless represents an advantageous plant architecture in pea breeding due to its ability to enhance resistance to lodging and potentially to powdery mildew. The introduction of semi-leafless pea varieties is considered a seminal advancement in pea breeding over the past half-century. The afila (af) mutation leads to the replacement of lateral leaflets by highly branched tendrils; combined with the semi-dwarfing le mutation, it forms the semi-leafless cultivated variety. In this study, we identified that mutations in two tandemly-arrayed genes encoding Cys(2)His(2) zinc finger transcription factors, PsPALM1a and PsPALM1b, were closely associated with the afila phenotype. These two genes may be deleted in the af mutant. In situ hybridization showed that both genes exhibit specific expression in early leaflet primordia. Furthermore, suppression of PsPALM1a/PsPALM1b resulted in a high frequency of conversion of lateral leaflets into tendrils. In conclusion, our study provides genetic evidence demonstrating that mutations in PsPALM1a and PsPALM1b are responsible for the af locus, contributing to a better understanding of compound leaf formation in peas and offering new insights for breeding applications related to afila.
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Affiliation(s)
- Zhuo Yuan
- Key Laboratory of Tropical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan Province, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoting Xie
- Key Laboratory of Tropical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan Province, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingli Liu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan Province, China
- College of Life Science, Southwest Forestry University, Kunming, China
| | - Yexin He
- Key Laboratory of Tropical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan Province, China
| | - Liangliang He
- Key Laboratory of Tropical Plant Resources and Sustainable Use, State Key Laboratory of Plant Diversity and Specialty Crops, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan Province, China
- University of Chinese Academy of Sciences, Beijing, China
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8
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Wu X, Hu Z, Zhang Y, Li M, Liao N, Dong J, Wang B, Wu J, Wu X, Wang Y, Wang J, Lu Z, Yang Y, Sun Y, Dong W, Zhang M, Li G. Differential selection of yield and quality traits has shaped genomic signatures of cowpea domestication and improvement. Nat Genet 2024; 56:992-1005. [PMID: 38649710 DOI: 10.1038/s41588-024-01722-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/19/2024] [Indexed: 04/25/2024]
Abstract
Cowpeas (tropical legumes) are important in ensuring food and nutritional security in developing countries, especially in sub-Saharan Africa. Herein, we report two high-quality genome assemblies of grain and vegetable cowpeas and we re-sequenced 344 accessions to characterize the genomic variations landscape. We identified 39 loci for ten important agronomic traits and more than 541 potential loci that underwent selection during cowpea domestication and improvement. In particular, the synchronous selections of the pod-shattering loci and their neighboring stress-relevant loci probably led to the enhancement of pod-shattering resistance and the compromise of stress resistance during the domestication from grain to vegetable cowpeas. Moreover, differential selections on multiple loci associated with pod length, grain number per pod, seed weight, pod and seed soluble sugars, and seed crude proteins shaped the yield and quality diversity in cowpeas. Our findings provide genomic insights into cowpea domestication and improvement footprints, enabling further genome-informed cultivar improvement of cowpeas.
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Affiliation(s)
- Xinyi Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Zhongyuan Hu
- Laboratory of Vegetable Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China
| | - Yan Zhang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China
| | - Mao Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Nanqiao Liao
- Laboratory of Vegetable Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China
| | - Junyang Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Baogen Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Xiaohua Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Ying Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Jian Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Zhongfu Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Yi Yang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China
| | - Yuyan Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Wenqi Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Mingfang Zhang
- Laboratory of Vegetable Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China.
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya, P. R. China.
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou, P. R. China.
| | - Guojing Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China.
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China.
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9
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Martínez-Fernández I, Fourquin C, Lindsay D, Berbel A, Balanzà V, Huang S, Dalmais M, LeSignor C, Bendahmane A, Warkentin TD, Madueño F, Ferrándiz C. Analysis of pea mutants reveals the conserved role of FRUITFULL controlling the end of flowering and its potential to boost yield. Proc Natl Acad Sci U S A 2024; 121:e2321975121. [PMID: 38557190 PMCID: PMC11009629 DOI: 10.1073/pnas.2321975121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
Monocarpic plants have a single reproductive phase in their life. Therefore, flower and fruit production are restricted to the length of this period. This reproductive strategy involves the regulation of flowering cessation by a coordinated arrest of the growth of the inflorescence meristems, optimizing resource allocation to ensure seed filling. Flowering cessation appears to be a regulated phenomenon in all monocarpic plants. Early studies in several species identified seed production as a major factor triggering inflorescence proliferative arrest. Recently, genetic factors controlling inflorescence arrest, in parallel to the putative signals elicited by seed production, have started to be uncovered in Arabidopsis, with the MADS-box gene FRUITFULL (FUL) playing a central role in the process. However, whether the genetic network regulating arrest is also at play in other species is completely unknown. Here, we show that this role of FUL is not restricted to Arabidopsis but is conserved in another monocarpic species with a different inflorescence structure, field pea, strongly suggesting that the network controlling the end of flowering is common to other plants. Moreover, field trials with lines carrying mutations in pea FUL genes show that they could be used to boost crop yield.
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Affiliation(s)
- Irene Martínez-Fernández
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia46022, Spain
| | - Chloe Fourquin
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia46022, Spain
| | - Donna Lindsay
- Department of Plant Sciences, College of Agriculture and Bio-Resources, University of Saskatchewan, Saskatoon, SKS7N5A8, Canada
| | - Ana Berbel
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia46022, Spain
| | - Vicente Balanzà
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia46022, Spain
| | - Shaoming Huang
- Department of Plant Sciences, College of Agriculture and Bio-Resources, University of Saskatchewan, Saskatoon, SKS7N5A8, Canada
| | - Marion Dalmais
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette91190, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette91190, France
| | - Christine LeSignor
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Dijon21000, France
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette91190, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette91190, France
| | - Thomas D. Warkentin
- Department of Plant Sciences, College of Agriculture and Bio-Resources, University of Saskatchewan, Saskatoon, SKS7N5A8, Canada
| | - Francisco Madueño
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia46022, Spain
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Valencia46022, Spain
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10
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Xie L, Gong X, Yang K, Huang Y, Zhang S, Shen L, Sun Y, Wu D, Ye C, Zhu QH, Fan L. Technology-enabled great leap in deciphering plant genomes. NATURE PLANTS 2024; 10:551-566. [PMID: 38509222 DOI: 10.1038/s41477-024-01655-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021-2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades. Substantial advances in read length, throughput, accuracy and cost-effectiveness have notably simplified the achievement of high-quality assemblies. Moreover, the development of multiple software tools using different algorithms offers the opportunity to generate more complete and complex assemblies. A database named N3: plants, genomes, technologies has been developed to accommodate the metadata associated with the 3,517 genomes that have been sequenced from 1,575 plant species since 2000. We also provide an outlook for emerging opportunities in plant genome sequencing.
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Affiliation(s)
- Lingjuan Xie
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yazhou Bay, Shanya, China
| | - Xiaojiao Gong
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Kun Yang
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Yujie Huang
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Shiyu Zhang
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Leti Shen
- Hainan Institute of Zhejiang University, Yazhou Bay, Shanya, China
| | - Yanqing Sun
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Dongya Wu
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Chuyu Ye
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, Black Mountain Laboratories, Canberra, Australia
| | - Longjiang Fan
- Institute of Crop Sciences & Institute of Bioinformatics, Zhejiang University, Hangzhou, China.
- Hainan Institute of Zhejiang University, Yazhou Bay, Shanya, China.
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11
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Feng L, Teng F, Li N, Zhang JC, Zhang BJ, Tsai SN, Yue XL, Gu LF, Meng GH, Deng TQ, Tong SW, Wang CM, Li Y, Shi W, Zeng YL, Jiang YM, Yu W, Ngai SM, An LZ, Lam HM, He JX. A reference-grade genome of the xerophyte Ammopiptanthus mongolicus sheds light on its evolution history in legumes and drought-tolerance mechanisms. PLANT COMMUNICATIONS 2024:100891. [PMID: 38561965 DOI: 10.1016/j.xplc.2024.100891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 02/26/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Plants that grow in extreme environments represent unique sources of stress-resistance genes and mechanisms. Ammopiptanthus mongolicus (Leguminosae) is a xerophytic evergreen broadleaf shrub native to semi-arid and desert regions; however, its drought-tolerance mechanisms remain poorly understood. Here, we report the assembly of a reference-grade genome for A. mongolicus, describe its evolutionary history within the legume family, and examine its drought-tolerance mechanisms. The assembled genome is 843.07 Mb in length, with 98.7% of the sequences successfully anchored to the nine chromosomes of A. mongolicus. The genome is predicted to contain 47 611 protein-coding genes, and 70.71% of the genome is composed of repetitive sequences; these are dominated by transposable elements, particularly long-terminal-repeat retrotransposons. Evolutionary analyses revealed two whole-genome duplication (WGD) events at 130 and 58 million years ago (mya) that are shared by the genus Ammopiptanthus and other legumes, but no species-specific WGDs were found within this genus. Ancestral genome reconstruction revealed that the A. mongolicus genome has undergone fewer rearrangements than other genomes in the legume family, confirming its status as a "relict plant". Transcriptomic analyses demonstrated that genes involved in cuticular wax biosynthesis and transport are highly expressed, both under normal conditions and in response to polyethylene glycol-induced dehydration. Significant induction of genes related to ethylene biosynthesis and signaling was also observed in leaves under dehydration stress, suggesting that enhanced ethylene response and formation of thick waxy cuticles are two major mechanisms of drought tolerance in A. mongolicus. Ectopic expression of AmERF2, an ethylene response factor unique to A. mongolicus, can markedly increase the drought tolerance of transgenic Arabidopsis thaliana plants, demonstrating the potential for application of A. mongolicus genes in crop improvement.
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Affiliation(s)
- Lei Feng
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China; Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Fei Teng
- BGI-Shenzhen Tech Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Na Li
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Jia-Cheng Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Bian-Jiang Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Sau-Na Tsai
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Xiu-Le Yue
- School of Life Sciences and Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou 730030, China
| | - Li-Fei Gu
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Guang-Hua Meng
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Tian-Quan Deng
- BGI-Shenzhen Tech Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Suk-Wah Tong
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Chun-Ming Wang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Yan Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Wei Shi
- BGI-Shenzhen Tech Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Yong-Lun Zeng
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yue-Ming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Weichang Yu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Sai-Ming Ngai
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Li-Zhe An
- School of Life Sciences and Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou 730030, China; State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China.
| | - Hon-Ming Lam
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China.
| | - Jun-Xian He
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China.
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12
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Wang Y, Tang H, Wang X, Sun Y, Joseph PV, Paterson AH. Detection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX. Nat Protoc 2024:10.1038/s41596-024-00968-2. [PMID: 38491145 DOI: 10.1038/s41596-024-00968-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 12/20/2023] [Indexed: 03/18/2024]
Abstract
As different taxa evolve, gene order often changes slowly enough that chromosomal 'blocks' with conserved gene orders (synteny) are discernible. The MCScanX toolkit ( https://github.com/wyp1125/MCScanX ) was published in 2012 as freely available software for the detection of such 'colinear blocks' and subsequent synteny and evolutionary analyses based on genome-wide gene location and protein sequence information. Owing to its simplicity and high efficiency for colinear block detection, MCScanX provides a powerful tool for conducting diverse synteny and evolutionary analyses. Moreover, the detection of colinear blocks has been embraced as an integral step for pangenome graph construction. Here, new application trends of MCScanX are explored, striving to better connect this increasingly used tool to other tools and accelerate insight generation from exponentially growing sequence data. We provide a detailed protocol that covers how to install MCScanX on diverse platforms, tune parameters, prepare input files from data from the National Center for Biotechnology Information, run MCScanX and its visualization and evolutionary analysis tools, and connect MCScanX with external tools, including MCScanX-transposed, Circos and SynVisio. This protocol is easily implemented by users with minimal computational background and is adaptable to new data of interest to them. The data and utility programs for this protocol can be obtained from http://bdx-consulting.com/mcscanx-protocol .
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Affiliation(s)
- Yupeng Wang
- BDX Research & Consulting LLC, Herndon, VA, USA
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA
| | - Haibao Tang
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA
- Center for Genomics, College of Science, North China University of Science and Technology, Tangshan, China
| | - Ying Sun
- BDX Research & Consulting LLC, Herndon, VA, USA
| | - Paule V Joseph
- Section of Sensory Science and Metabolism, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, USA.
- National Institute of Nursing Research, Bethesda, MD, USA.
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA, USA.
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13
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Chen B, Shi Y, Sun Y, Lu L, Wang L, Liu Z, Cheng S. Innovations in functional genomics and molecular breeding of pea: exploring advances and opportunities. ABIOTECH 2024; 5:71-93. [PMID: 38576433 PMCID: PMC10987475 DOI: 10.1007/s42994-023-00129-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/05/2023] [Indexed: 04/06/2024]
Abstract
The garden pea (Pisum sativum L.) is a significant cool-season legume, serving as crucial food sources, animal feed, and industrial raw materials. The advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea breeding. Notably, the release of the pea reference genome has enhanced our understanding of plant architecture, symbiotic nitrogen fixation (SNF), flowering time, floral organ development, seed development, and stress resistance. However, a considerable gap remains between pea functional genomics and molecular breeding. This review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.
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Affiliation(s)
- Baizhi Chen
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Yan Shi
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Yuchen Sun
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Lu Lu
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Luyao Wang
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Zijian Liu
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Shifeng Cheng
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
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14
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Wang P, Jin M, Wu C, Peng Y, He Y, Wang H, Xiao Y. Population genomics of Agrotis segetum provide insights into the local adaptive evolution of agricultural pests. BMC Biol 2024; 22:42. [PMID: 38378556 PMCID: PMC10877822 DOI: 10.1186/s12915-024-01844-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/12/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND The adaptive mechanisms of agricultural pests are the key to understanding the evolution of the pests and to developing new control strategies. However, there are few studies on the genetic basis of adaptations of agricultural pests. The turnip moth, Agrotis segetum (Lepidoptera: Noctuidae) is an important underground pest that affects a wide range of host plants and has a strong capacity to adapt to new environments. It is thus a good model for studying the adaptive evolution of pest species. RESULTS We assembled a high-quality reference genome of A. segetum using PacBio reads. Then, we constructed a variation map of A. segetum by resequencing 98 individuals collected from six natural populations in China. The analysis of the population structure showed that all individuals were divided into four well-differentiated populations, corresponding to their geographical distribution. Selective sweep analysis and environmental association studies showed that candidate genes associated with local adaptation were functionally correlated with detoxification metabolism and glucose metabolism. CONCLUSIONS Our study of A. segetum has provided insights into the genetic mechanisms of local adaptation and evolution; it has also produced genetic resources for developing new pest management strategies.
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Affiliation(s)
- Ping Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan university, Shenzhen, 518000, China
| | - Minghui Jin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chao Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yanjin He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan university, Shenzhen, 518000, China
| | - Hanyue Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yutao Xiao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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15
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Xiong R, Peng Z, Zhou H, Xue G, He A, Yao X, Weng W, Wu W, Ma C, Bai Q, Ruan J. Genome-wide identification, structural characterization and gene expression analysis of the WRKY transcription factor family in pea (Pisum sativum L.). BMC PLANT BIOLOGY 2024; 24:113. [PMID: 38365619 PMCID: PMC10870581 DOI: 10.1186/s12870-024-04774-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/29/2024] [Indexed: 02/18/2024]
Abstract
BACKGROUND The WRKY gene family is one of the largest families of transcription factors in higher plants, and WRKY transcription factors play important roles in plant growth and development as well as in response to abiotic stresses; however, the WRKY gene family in pea has not been systematically reported. RESULTS In this study, 89 pea WRKY genes were identified and named according to the random distribution of PsWRKY genes on seven chromosomes. The gene family was found to have nine pairs of tandem duplicates and 19 pairs of segment duplicates. Phylogenetic analyses of the PsWRKY and 60 Arabidopsis WRKY proteins were performed to determine their homology, and the PsWRKYs were classified into seven subfamilies. Analysis of the physicochemical properties, motif composition, and gene structure of pea WRKYs revealed significant differences in the physicochemical properties within the PsWRKY family; however, their gene structure and protein-conserved motifs were highly conserved among the subfamilies. To further investigate the evolutionary relationships of the PsWRKY family, we constructed comparative syntenic maps of pea with representative monocotyledonous and dicotyledonous plants and found that it was most recently homologous to the dicotyledonous WRKY gene families. Cis-acting element analysis of PsWRKY genes revealed that this gene family can respond to hormones, such as abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellin (GA), methyl jasmonate (MeJA), and salicylic acid (SA). Further analysis of the expression of 14 PsWRKY genes from different subfamilies in different tissues and fruit developmental stages, as well as under five different hormone treatments, revealed differences in their expression patterns in the different tissues and fruit developmental stages, as well as under hormone treatments, suggesting that PsWRKY genes may have different physiological functions and respond to hormones. CONCLUSIONS In this study, we systematically identified WRKY genes in pea for the first time and further investigated their physicochemical properties, evolution, and expression patterns, providing a theoretical basis for future studies on the functional characterization of pea WRKY genes during plant growth and development.
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Affiliation(s)
- Ruiqi Xiong
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Zhonghua Peng
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Hui Zhou
- Sichuan Province Seed Station, Chengdu, Sichuan, 610041, China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Xin Yao
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Wenfeng Weng
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Weijiao Wu
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Chao Ma
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Qing Bai
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, P R China.
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16
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Lavaud C, Lesné A, Leprévost T, Pilet-Nayel ML. Fine mapping of Ae-Ps4.5, a major locus for resistance to pathotype III of Aphanomyces euteiches in pea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:47. [PMID: 38334777 DOI: 10.1007/s00122-024-04548-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
KEY MESSAGE QTL mapping and recombinant screening confirmed the major effect of QTL Ae-Ps4.5 on pea resistance to pathotype III of Aphanomyces euteiches and fine-mapped the QTL to a 3.06-Mb interval. Aphanomyces root rot, caused by Aphanomyces euteiches, is the most important disease of pea (Pisum sativum L.) worldwide. The development of pea-resistant varieties is a major challenge to control the disease. Previous linkage studies identified seven main resistance quantitative trait loci (QTL), including the QTL Ae-Ps4.5 associated with partial resistance in US nurseries infested by the pea pathotype III of A. euteiches. This study aimed to confirm the major effect of Ae-Ps4.5 on A. euteiches pathotype III, refine its interval, and identify candidate genes underlying the QTL. QTL mapping on an updated genetic map from the Puget × 90-2079 pea recombinant inbred line population identified Ae-Ps4.5 in a 0.8-cM confidence interval with a high effect (R2 = 89%) for resistance to the Ae109 reference strain of A. euteiches (pathotype III) under controlled conditions. However, the QTL mapping did not detect Ae-Ps4.5 for resistance to the RB84 reference strain of A. euteiches (pathotype I). Screening 224-pea BC5F2 plant progeny derived from three near-isogenic lines (NILs) carrying the 90-2079 allele at Ae-Ps4.5 in the Puget genetic background with 26 SNP markers identified 15 NILs showing recombination in the QTL interval. Phenotyping of the recombinant lines for resistance to the Ae109 strain of A. euteiches reduced the QTL to a physical interval of 3.06 Mb, containing 50 putative annotated genes on the Caméor pea genome V1a among which three candidate genes highlighted. This study provides closely linked SNP markers and putative candidate genes to accelerate pea breeding for resistant varieties to Aphanomyces root rot.
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Affiliation(s)
- Clément Lavaud
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Angélique Lesné
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Théo Leprévost
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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17
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Li H, Peng Y, Wu C, Li Z, Zou L, Mao K, Ping J, Buck R, Monahan S, Sethuraman A, Xiao Y. Assessing genome-wide adaptations associated with range expansion in the pink rice borer, Sesamia inferens. INSECT SCIENCE 2024. [PMID: 38204333 DOI: 10.1111/1744-7917.13320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/20/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Understanding the genetic basis of adaptive evolution following habitat expansion can have important implications for pest management. The pink rice borer (PRB), Sesamia inferens (Walker), is a destructive pest of rice that was historically restricted to regions south of 34° N latitude in China. However, with changes in global climate and farming practices, the distribution of this moth has progressively expanded, encompassing most regions in North China. Here, 3 highly differentiated subpopulations were discovered using high-quality single-nucleotide polymorphism and structural variant datasets across China, corresponding to northern, southern China regions, and the Yunnan-Guizhou Plateau, with significant patterns of isolation by geographic and environmental distances. Our estimates of evolutionary history indicate asymmetric migration with varying population sizes across the 3 subpopulations. Selective sweep analyses estimated strong selection at insect cuticle glycine-rich cuticular protein genes which are associated with enhanced desiccation adaptability in the northern group, and at the histone-lysine-N-methyltransferase gene associated with range expansion and local adaptation in the Shandong population. Our findings have significant implications for the development of effective strategies to control this pest.
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Affiliation(s)
- Hongran Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Yan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Chao Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Zhimin Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Luming Zou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Kaikai Mao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Junfen Ping
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Ryan Buck
- Department of Biology, San Diego State University, CA, USA
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Scott Monahan
- Department of Biology, San Diego State University, CA, USA
| | | | - Yutao Xiao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
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18
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Luo H, Wang X, You C, Wu X, Pan D, Lv Z, Li T, Zhang D, Shen Z, Zhang X, Liu G, He K, Ye Q, Jia Y, Zhao Q, Deng X, Cao X, Song X, Huang G. Telomere-to-telomere genome of the allotetraploid legume Sesbania cannabina reveals transposon-driven subgenome divergence and mechanisms of alkaline stress tolerance. SCIENCE CHINA. LIFE SCIENCES 2024; 67:149-160. [PMID: 37897613 DOI: 10.1007/s11427-023-2463-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/10/2023] [Indexed: 10/30/2023]
Abstract
Alkaline soils pose an increasing problem for agriculture worldwide, but using stress-tolerant plants as green manure can improve marginal land. Here, we show that the legume Sesbania cannabina is very tolerant to alkaline conditions and, when used as a green manure, substantially improves alkaline soil. To understand genome evolution and the mechanisms of stress tolerance in this allotetraploid legume, we generated the first telomere-to-telomere genome assembly of S. cannabina spanning ∼2,087 Mb. The assembly included all centromeric regions, which contain centromeric satellite repeats, and complete chromosome ends with telomeric characteristics. Further genome analysis distinguished A and B subgenomes, which diverged approximately 7.9 million years ago. Comparative genomic analysis revealed that the chromosome homoeologs underwent large-scale inversion events (>10 Mb) and a significant, transposon-driven size expansion of the chromosome 5A homoeolog. We further identified four specific alkali-induced phosphate transporter genes in S. cannabina; these may function in alkali tolerance by relieving the deficiency in available phosphorus in alkaline soil. Our work highlights the significance of S. cannabina as a green tool to improve marginal lands and sheds light on subgenome evolution and adaptation to alkaline soils.
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Affiliation(s)
- Haofei Luo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofei Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Changqing You
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuedan Wu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Duofeng Pan
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Zhiyao Lv
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Tong Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dongmei Zhang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Zhongbao Shen
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xiaodong Zhang
- Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, 257345, China
- Shandong Green Manure Ecological Technology Co., Ltd, Dongying, 257345, China
| | - Guodao Liu
- State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Kaixuan He
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Qingtong Ye
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yajun Jia
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Qinghua Zhao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Gai Huang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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19
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Skiba E, Pietrzak M, Michlewska S, Gruszka J, Malejko J, Godlewska-Żyłkiewicz B, Wolf WM. Photosynthesis governed by nanoparticulate titanium dioxide. The Pisum sativum L. case study. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122735. [PMID: 37848082 DOI: 10.1016/j.envpol.2023.122735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023]
Abstract
Wide availability of anthropogenic TiO2 nanoparticles facilitates their penetration into environment and prompts interactions with plants. They alter plants growth and change their nutritional status. In particular, metabolic processes are affected. In this work the effect of nanometric TiO2 on photosynthesis efficiency in green pea (Pisum sativum L.) was studied. Hydroponic cultivations with three Ti levels (10; 50 and 100 mg L-1) were applied. At all concentrations nanoparticles penetrated into plant tissues and were detected by the single particle ICP-MS/MS method. Nanoparticles altered the CO2 assimilation rate and gas exchange parameters (i.e. transpiration, stomatal conductance, sub-stomatal CO2 concentration). The most pronounced effects were observed for Ti 50 mg L-1 cultivation where photosynthesis efficiency, transpiration and stomatal conductance were increased by 14.69%, 4.58% and 8.92%, respectively. They were further confirmed by high maximum ribulose 1,5-bisphosphate carboxylation rate (27.40% increase), maximum electron transport rate (21.51% increase) and the lowest CO2 compensation point (45.19% decrease). Furthermore, concentrations of Cu, Mn, Zn, Fe, Mg, Ca, K and P were examined with the most pronounced changes observed for elements directly involved in photosynthesis (Cu, Zn, Mn, and Fe). The Cu concentrations in roots, stems and leaves for Ti 50 mg L-1 cultivation were below the control by 33.15%, 38.28% and 10.76%, respectively. The Zn content in analogous treatment and organs decreased by 30.24%, 26.69% and 13.35%. The Mn and Fe levels in leaves were increased by 72.22% and 50.32%, respectively. Our results indicated that plant defence mechanisms which restrain the water uptake have been overcome in pea by photocatalytic activity of nanoparticulate TiO2 which stimulated photosynthesis. On the contrary to the substantial stomatal conductance, the transpiration has been reduced because exceptional part of water flow was already consumed in chloroplasts and could not have been freed to the atmosphere.
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Affiliation(s)
- Elżbieta Skiba
- Institute of General and Ecological Chemistry, Lodz University of Technology, Poland.
| | - Monika Pietrzak
- Institute of General and Ecological Chemistry, Lodz University of Technology, Poland
| | - Sylwia Michlewska
- Faculty of Biology and Environmental Protection, Laboratory of Microscopic Imaging and Specialized Biological Techniques, University of Lodz, Poland
| | - Jakub Gruszka
- Department of Analytical and Inorganic Chemistry, Faculty of Chemistry, University of Bialystok, Poland
| | - Julita Malejko
- Department of Analytical and Inorganic Chemistry, Faculty of Chemistry, University of Bialystok, Poland
| | | | - Wojciech M Wolf
- Institute of General and Ecological Chemistry, Lodz University of Technology, Poland
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20
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Zhu P, He T, Zheng Y, Chen L. The need for masked genomes in gymnosperms. FRONTIERS IN PLANT SCIENCE 2023; 14:1309744. [PMID: 38146270 PMCID: PMC10749308 DOI: 10.3389/fpls.2023.1309744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023]
Affiliation(s)
| | | | | | - Lingyan Chen
- Fujian Agriculture and Forestry University, Fuzhou, China
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21
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Ellis N, Hofer J, Sizer-Coverdale E, Lloyd D, Aubert G, Kreplak J, Burstin J, Cheema J, Bal M, Chen Y, Deng S, Wouters RHM, Steuernagel B, Chayut N, Domoney C. Recombinant inbred lines derived from wide crosses in Pisum. Sci Rep 2023; 13:20408. [PMID: 37990072 PMCID: PMC10663473 DOI: 10.1038/s41598-023-47329-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/12/2023] [Indexed: 11/23/2023] Open
Abstract
Genomic resources are becoming available for Pisum but to link these to phenotypic diversity requires well marked populations segregating for relevant traits. Here we describe two such resources. Two recombinant inbred populations, derived from wide crosses in Pisum are described. One high resolution mapping population involves cv Caméor, for which the first pea whole genome assembly was obtained, crossed to JI0281, a basally divergent P. sativum sativum landrace from Ethiopia. The other is an inter sub-specific cross between P. s. sativum and the independently domesticated P. s. abyssinicum. The corresponding genetic maps provide information on chromosome level sequence assemblies and identify structural differences between the genomes of these two Pisum subspecies. In order to visualise chromosomal translocations that distinguish the mapping parents, we created a simplified version of Threadmapper to optimise it for interactive 3-dimensional display of multiple linkage groups. The genetic mapping of traits affecting seed coat roughness and colour, plant height, axil ring pigmentation, leaflet number and leaflet indentation enabled the definition of their corresponding genomic regions. The consequence of structural rearrangement for trait analysis is illustrated by leaf serration. These analyses pave the way for identification of the underlying genes and illustrate the utility of these publicly available resources. Segregating inbred populations derived from wide crosses in Pisum, together with the associated marker data, are made publicly available for trait dissection. Genetic analysis of these populations is informative about chromosome scale assemblies, structural diversity in the pea genome and has been useful for the fine mapping of several discrete and quantitative traits.
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Affiliation(s)
- N Ellis
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK.
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK.
| | - J Hofer
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
| | - E Sizer-Coverdale
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
- Germinal Horizon, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
| | - D Lloyd
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
- Germinal Horizon, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
| | - G Aubert
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - J Kreplak
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - J Burstin
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - J Cheema
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - M Bal
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Y Chen
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - S Deng
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - R H M Wouters
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - B Steuernagel
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - N Chayut
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - C Domoney
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
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22
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Delorean EE, Youngblood RC, Simpson SA, Schoonmaker AN, Scheffler BE, Rutter WB, Hulse-Kemp AM. Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning. FRONTIERS IN PLANT SCIENCE 2023; 14:1184112. [PMID: 38034563 PMCID: PMC10687446 DOI: 10.3389/fpls.2023.1184112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
As sequencing costs decrease and availability of high fidelity long-read sequencing increases, generating experiment specific de novo genome assemblies becomes feasible. In many crop species, obtaining the genome of a hybrid or heterozygous individual is necessary for systems that do not tolerate inbreeding or for investigating important biological questions, such as hybrid vigor. However, most genome assembly methods that have been used in plants result in a merged single sequence representation that is not a true biologically accurate representation of either haplotype within a diploid individual. The resulting genome assembly is often fragmented and exhibits a mosaic of the two haplotypes, referred to as haplotype-switching. Important haplotype level information, such as causal mutations and structural variation is therefore lost causing difficulties in interpreting downstream analyses. To overcome this challenge, we have applied a method developed for animal genome assembly called trio-binning to an intra-specific hybrid of chili pepper (Capsicum annuum L. cv. HDA149 x Capsicum annuum L. cv. HDA330). We tested all currently available softwares for performing trio-binning, combined with multiple scaffolding technologies including Bionano to determine the optimal method of producing the best haplotype-resolved assembly. Ultimately, we produced highly contiguous biologically true haplotype-resolved genome assemblies for each parent, with scaffold N50s of 266.0 Mb and 281.3 Mb, with 99.6% and 99.8% positioned into chromosomes respectively. The assemblies captured 3.10 Gb and 3.12 Gb of the estimated 3.5 Gb chili pepper genome size. These assemblies represent the complete genome structure of the intraspecific hybrid, as well as the two parental genomes, and show measurable improvements over the currently available reference genomes. Our manuscript provides a valuable guide on how to apply trio-binning to other plant genomes.
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Affiliation(s)
- Emily E. Delorean
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC, United States
- Crop and Soil Sciences Department, North Carolina State University, Raleigh, NC, United States
| | - Ramey C. Youngblood
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, United States
| | - Sheron A. Simpson
- Genomics and Bioinformatics Research Unit, United States Department of Agriculture - Agriculture Research Service (USDA-ARS), Stoneville, MS, United States
| | - Ashley N. Schoonmaker
- Crop and Soil Sciences Department, North Carolina State University, Raleigh, NC, United States
| | - Brian E. Scheffler
- Genomics and Bioinformatics Research Unit, United States Department of Agriculture - Agriculture Research Service (USDA-ARS), Stoneville, MS, United States
| | - William B. Rutter
- US Vegetable Laboratory, United States Department of Agriculture - Agriculture Research Service (USDA-ARS), Charleston, SC, United States
| | - Amanda M. Hulse-Kemp
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC, United States
- Crop and Soil Sciences Department, North Carolina State University, Raleigh, NC, United States
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23
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Xiao Y, Liu J, Wei J, Xiao Z, Li J, Ma Y. Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration. Sci Data 2023; 10:774. [PMID: 37935724 PMCID: PMC10630468 DOI: 10.1038/s41597-023-02699-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
Sciaenops ocellatus is among the most important artificially introduced farmed fish across 11 countries and regions. However, the frequent occurrence of extreme weather events and breeding escapes have placed great pressure on local marine biodiversity and ecosystems. We reported the de novo assembly and annotation with a contig N50 of 28.30 Mb using PacBio HiFi sequencing and Hi-C technologies, which resulted in a 283-fold increase in contig N50 length and improvement in continuity and quality in complex repetitive region for S. ocellatus compared to the previous version. In total, 257.36 Mb of repetitive sequences accounted for 35.48% of the genome, and 22,845 protein-coding genes associated with a BUSCO value of 98.32%, were identified by genome annotation. Moreover, 54 hub genes rapidly responding to hypoosmotic stress were identified by WGCNA. The high-quality chromosome-scale S. ocellatus genome and candidate resistance-related gene sets will not only provide a genomic basis for genetic improvement via molecular breeding, but will also lay an important foundation for investigating the molecular regulation of rapid responses to stress.
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Affiliation(s)
- Yongshuang Xiao
- Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jing Liu
- Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Jiehong Wei
- Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zhizhong Xiao
- Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jun Li
- Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Yuting Ma
- Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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24
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Aylward AJ, Petrus S, Mamerto A, Hartwick NT, Michael TP. PanKmer: k-mer-based and reference-free pangenome analysis. Bioinformatics 2023; 39:btad621. [PMID: 37846049 PMCID: PMC10603592 DOI: 10.1093/bioinformatics/btad621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/29/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023] Open
Abstract
SUMMARY Pangenomes are replacing single reference genomes as the definitive representation of DNA sequence within a species or clade. Pangenome analysis predominantly leverages graph-based methods that require computationally intensive multiple genome alignments, do not scale to highly complex eukaryotic genomes, limit their scope to identifying structural variants (SVs), or incur bias by relying on a reference genome. Here, we present PanKmer, a toolkit designed for reference-free analysis of pangenome datasets consisting of dozens to thousands of individual genomes. PanKmer decomposes a set of input genomes into a table of observed k-mers and their presence-absence values in each genome. These are stored in an efficient k-mer index data format that encodes SNPs, INDELs, and SVs. It also includes functions for downstream analysis of the k-mer index, such as calculating sequence similarity statistics between individuals at whole-genome or local scales. For example, k-mers can be "anchored" in any individual genome to quantify sequence variability or conservation at a specific locus. This facilitates workflows with various biological applications, e.g. identifying cases of hybridization between plant species. PanKmer provides researchers with a valuable and convenient means to explore the full scope of genetic variation in a population, without reference bias. AVAILABILITY AND IMPLEMENTATION PanKmer is implemented as a Python package with components written in Rust, released under a BSD license. The source code is available from the Python Package Index (PyPI) at https://pypi.org/project/pankmer/ as well as Gitlab at https://gitlab.com/salk-tm/pankmer. Full documentation is available at https://salk-tm.gitlab.io/pankmer/.
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Affiliation(s)
- Anthony J Aylward
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States
| | - Semar Petrus
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States
| | - Allen Mamerto
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States
| | - Nolan T Hartwick
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States
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25
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Wei M, Huang Y, Mo C, Wang H, Zeng Q, Yang W, Chen J, Zhang X, Kong Q. Telomere-to-telomere genome assembly of melon ( Cucumis melo L. var. inodorus) provides a high-quality reference for meta-QTL analysis of important traits. HORTICULTURE RESEARCH 2023; 10:uhad189. [PMID: 37915500 PMCID: PMC10615816 DOI: 10.1093/hr/uhad189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/12/2023] [Indexed: 11/03/2023]
Abstract
Melon is an important horticultural crop with extensive diversity in many horticultural groups. To explore its genomic diversity, it is necessary to assemble more high-quality complete genomes from different melon accessions. Meanwhile, a large number of QTLs have been mapped in several studies. Integration of the published QTLs onto a complete genome can provide more accurate information for candidate gene cloning. To address these problems, a telomere-to-telomere (T2T) genome of the elite melon landrace Kuizilikjiz (Cucumis melo L. var. inodorus) was de novo assembled and all the published QTLs were projected onto it in this study. The results showed that a high-quality Kuizilikjiz genome with the size of 379.2 Mb and N50 of 31.7 Mb was de novo assembled using the combination of short reads, PacBio high-fidelity long reads, Hi-C data, and a high-density genetic map. Each chromosome contained the centromere and telomeres at both ends. A large number of structural variations were observed between Kuizilikjiz and the other published genomes. A total of 1294 QTLs published in 67 studies were collected and projected onto the T2T genome. Several clustered, co-localized, and overlapped QTLs were determined. Furthermore, 20 stable meta-QTLs were identified, which significantly reduced the mapping intervals of the initial QTLs and greatly facilitated identification of the candidate genes. Collectively, the T2T genome assembly together with the numerous projected QTLs will not only broaden the high-quality genome resources but also provide valuable and abundant QTL information for cloning the genes controlling important traits in melon.
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Affiliation(s)
- Minghua Wei
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Huang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Changjuan Mo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Haiyan Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingguo Zeng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Yang
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Jihao Chen
- Hainan Sanya Experimental Center for Crop Breeding, Xinjiang Academy of Agricultural Sciences, Sanya 572014, China
| | - Xuejun Zhang
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Hainan Sanya Experimental Center for Crop Breeding, Xinjiang Academy of Agricultural Sciences, Sanya 572014, China
| | - Qiusheng Kong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
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van Dijk EL, Naquin D, Gorrichon K, Jaszczyszyn Y, Ouazahrou R, Thermes C, Hernandez C. Genomics in the long-read sequencing era. Trends Genet 2023; 39:649-671. [PMID: 37230864 DOI: 10.1016/j.tig.2023.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
Long-read sequencing (LRS) technologies have provided extremely powerful tools to explore genomes. While in the early years these methods suffered technical limitations, they have recently made significant progress in terms of read length, throughput, and accuracy and bioinformatics tools have strongly improved. Here, we aim to review the current status of LRS technologies, the development of novel methods, and the impact on genomics research. We will explore the most impactful recent findings made possible by these technologies focusing on high-resolution sequencing of genomes and transcriptomes and the direct detection of DNA and RNA modifications. We will also discuss how LRS methods promise a more comprehensive understanding of human genetic variation, transcriptomics, and epigenetics for the coming years.
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Affiliation(s)
- Erwin L van Dijk
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Kévin Gorrichon
- National Center of Human Genomics Research (CNRGH), 91000 Évry-Courcouronnes, France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Rania Ouazahrou
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Claude Thermes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Céline Hernandez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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27
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Osuna-Caballero S, Olivoto T, Jiménez-Vaquero MA, Rubiales D, Rispail N. RGB image-based method for phenotyping rust disease progress in pea leaves using R. PLANT METHODS 2023; 19:86. [PMID: 37605206 PMCID: PMC10440949 DOI: 10.1186/s13007-023-01069-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Rust is a damaging disease affecting vital crops, including pea, and identifying highly resistant genotypes remains a challenge. Accurate measurement of infection levels in large germplasm collections is crucial for finding new resistance sources. Current evaluation methods rely on visual estimation of disease severity and infection type under field or controlled conditions. While they identify some resistance sources, they are error-prone and time-consuming. An image analysis system proves useful, providing an easy-to-use and affordable way to quickly count and measure rust-induced pustules on pea samples. This study aimed to develop an automated image analysis pipeline for accurately calculating rust disease progression parameters under controlled conditions, ensuring reliable data collection. RESULTS A highly efficient and automatic image-based method for assessing rust disease in pea leaves was developed using R. The method's optimization and validation involved testing different segmentation indices and image resolutions on 600 pea leaflets with rust symptoms. The approach allows automatic estimation of parameters like pustule number, pustule size, leaf area, and percentage of pustule coverage. It reconstructs time series data for each leaf and integrates daily estimates into disease progression parameters, including latency period and area under the disease progression curve. Significant variation in disease responses was observed between genotypes using both visual ratings and image-based analysis. Among assessed segmentation indices, the Normalized Green Red Difference Index (NGRDI) proved fastest, analysing 600 leaflets at 60% resolution in 62 s with parallel processing. Lin's concordance correlation coefficient between image-based and visual pustule counting showed over 0.98 accuracy at full resolution. While lower resolution slightly reduced accuracy, differences were statistically insignificant for most disease progression parameters, significantly reducing processing time and storage space. NGRDI was optimal at all time points, providing highly accurate estimations with minimal accumulated error. CONCLUSIONS A new image-based method for monitoring pea rust disease in detached leaves, using RGB spectral indices segmentation and pixel value thresholding, improves resolution and precision. It rapidly analyses hundreds of images with accuracy comparable to visual methods and higher than other image-based approaches. This method evaluates rust progression in pea, eliminating rater-induced errors from traditional methods. Implementing this approach to evaluate large germplasm collections will improve our understanding of plant-pathogen interactions and aid future breeding for novel pea cultivars with increased rust resistance.
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Affiliation(s)
| | - Tiago Olivoto
- Department of Plant Science, Federal University of Santa Catarina, Florianópolis, 88034-000, SC, Brazil
| | | | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Av. Menéndez Pidal s/n 14004, Córdoba, Spain
| | - Nicolas Rispail
- Institute for Sustainable Agriculture, CSIC, Av. Menéndez Pidal s/n 14004, Córdoba, Spain
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28
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Varshney RK. Meet the PCP Editor-Rajeev K. Varshney FRS. PLANT & CELL PHYSIOLOGY 2023; 64:841-843. [PMID: 37338338 PMCID: PMC10434731 DOI: 10.1093/pcp/pcad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/12/2023] [Accepted: 06/17/2023] [Indexed: 06/21/2023]
Affiliation(s)
- Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA 6150, Australia
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29
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Li H, Song K, Zhang X, Wang D, Dong S, Liu Y, Yang L. Application of Multi-Perspectives in Tea Breeding and the Main Directions. Int J Mol Sci 2023; 24:12643. [PMID: 37628823 PMCID: PMC10454712 DOI: 10.3390/ijms241612643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/29/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Tea plants are an economically important crop and conducting research on tea breeding contributes to enhancing the yield and quality of tea leaves as well as breeding traits that satisfy the requirements of the public. This study reviews the current status of tea plants germplasm resources and their utilization, which has provided genetic material for the application of multi-omics, including genomics and transcriptomics in breeding. Various molecular markers for breeding were designed based on multi-omics, and available approaches in the direction of high yield, quality and resistance in tea plants breeding are proposed. Additionally, future breeding of tea plants based on single-cellomics, pangenomics, plant-microbe interactions and epigenetics are proposed and provided as references. This study aims to provide inspiration and guidance for advancing the development of genetic breeding in tea plants, as well as providing implications for breeding research in other crops.
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Affiliation(s)
| | | | | | | | | | | | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China
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30
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Imbert B, Kreplak J, Flores RG, Aubert G, Burstin J, Tayeh N. Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes. Front Artif Intell 2023; 6:1191122. [PMID: 37601035 PMCID: PMC10435283 DOI: 10.3389/frai.2023.1191122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
While the continuing decline in genotyping and sequencing costs has largely benefited plant research, some key species for meeting the challenges of agriculture remain mostly understudied. As a result, heterogeneous datasets for different traits are available for a significant number of these species. As gene structures and functions are to some extent conserved through evolution, comparative genomics can be used to transfer available knowledge from one species to another. However, such a translational research approach is complex due to the multiplicity of data sources and the non-harmonized description of the data. Here, we provide two pipelines, referred to as structural and functional pipelines, to create a framework for a NoSQL graph-database (Neo4j) to integrate and query heterogeneous data from multiple species. We call this framework Orthology-driven knowledge base framework for translational research (Ortho_KB). The structural pipeline builds bridges across species based on orthology. The functional pipeline integrates biological information, including QTL, and RNA-sequencing datasets, and uses the backbone from the structural pipeline to connect orthologs in the database. Queries can be written using the Neo4j Cypher language and can, for instance, lead to identify genes controlling a common trait across species. To explore the possibilities offered by such a framework, we populated Ortho_KB to obtain OrthoLegKB, an instance dedicated to legumes. The proposed model was evaluated by studying the conservation of a flowering-promoting gene. Through a series of queries, we have demonstrated that our knowledge graph base provides an intuitive and powerful platform to support research and development programmes.
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Affiliation(s)
- Baptiste Imbert
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Jonathan Kreplak
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Raphaël-Gauthier Flores
- Université Paris-Saclay, INRAE, URGI, Versailles, France
- Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, Versailles, France
| | - Grégoire Aubert
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Judith Burstin
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Nadim Tayeh
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
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31
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Li X, Ou M, Li L, Li Y, Feng Y, Huang X, Baluška F, Shabala S, Yu M, Shi W, Wu F. The wall-associated kinase gene family in pea (Pisum sativum) and its function in response to B deficiency and Al toxicity. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154045. [PMID: 37356321 DOI: 10.1016/j.jplph.2023.154045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/18/2023] [Accepted: 06/18/2023] [Indexed: 06/27/2023]
Abstract
Plant cell walls are embedded in a pectin matrix which is physically linked with the wall-associated kinases (WAKs), a subfamily of receptor-like kinases that participate in the cell wall integrity (CWI) sensing. Since cell walls are also the main binding sites for boron (B) and aluminum (Al), WAK may be potentially associated with the regulation of plant responses to Al toxicity and B deficiency. Using pea as a model species, we have identified a total of 28 WAK genes in the genome and named them according to its chromosomal location. All the PsWAKs were phylogenetically grouped into three clades. Phylogenetic relationship and synteny analysis showed that the PsWAKs in pea and Glycine max or Medicago truncatula shared a relatively conserved evolutionary history. Protein domain, motif, and transmembrane analysis indicated that all PsWAK proteins were predicted to be localized to the plasma membrane, and most PsWAKs shared a similar structure to their homologs. The RNA-seq data showed that the expression pattern of WAK genes in response to B deficiency was similar to that of Al toxicity, with most of PsWAKs being up-regulated. The qRT-PCR results further confirmed that PsWAK5, PsWAK9 and PsWAK14 were more specific for both B-deficiency and Al toxicity, and the expression levels of PsWAK5, PsWAK9 and PsWAK14 were significantly higher in the Al-sensitive cultivar Hyogo than in the Al-resistant cultivar Alaska under Al toxicity. This study provided an important basis for the functional and evolutionary analysis of PsWAKs and linked them to responses to cell wall damage induced by B-deficiency and Al toxicity, suggesting that PsWAKs may play a key role in the perception of cell wall integrity under Al toxicity or B-deficiency, as well as in the regulation of Al tolerance in pea.
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Affiliation(s)
- Xuewen Li
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China
| | - Meiyin Ou
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China
| | - Li Li
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China
| | - Yalin Li
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China
| | - Yingming Feng
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China
| | - Xin Huang
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China
| | - František Baluška
- Institute of Cellular and Molecular Botany, University of Bonn, D-53115, Bonn, Germany
| | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China; School of Biological Science, University of Western Australia, Crawley, WA 6009, Australia
| | - Min Yu
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China
| | - Weiming Shi
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Feihua Wu
- International Research Centre for Environmental Membrane Biology& Department of Horticulture, Foshan University, 528000, China.
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Delvento C, Arcieri F, Marcotrigiano AR, Guerriero M, Fanelli V, Dellino M, Curci PL, Bouwmeester H, Lotti C, Ricciardi L, Pavan S. High-density linkage mapping and genetic dissection of resistance to broomrape ( Orobanche crenata Forsk.) in pea ( Pisum sativum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1216297. [PMID: 37492777 PMCID: PMC10364127 DOI: 10.3389/fpls.2023.1216297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/21/2023] [Indexed: 07/27/2023]
Abstract
Pea (Pisum sativum L.) is a widely cultivated legume of major importance for global food security and agricultural sustainability. Crenate broomrape (Orobanche crenata Forsk.) (Oc) is a parasitic weed severely affecting legumes, including pea, in the Mediterranean Basin and the Middle East. Previously, the identification of the pea line "ROR12", displaying resistance to Oc, was reported. Two-year field trials on a segregant population of 148 F7 recombinant inbred lines (RILs), originating from a cross between "ROR12" and the susceptible cultivar "Sprinter", revealed high heritability (0.84) of the "ROR12" resistance source. Genotyping-by-sequencing (GBS) on the same RIL population allowed the construction of a high-density pea linkage map, which was compared with the pea reference genome and used for quantitative trait locus (QTL) mapping. Three QTLs associated with the response to Oc infection, named PsOcr-1, PsOcr-2, and PsOcr-3, were identified, with PsOcr-1 explaining 69.3% of the genotypic variance. Evaluation of the effects of different genotypic combinations indicated additivity between PsOcr-1 and PsOcr-2, and between PsOcr-1 and PsOcr-3, and epistasis between PsOcr-2 and PsOcr-3. Finally, three Kompetitive Allele Specific PCR (KASP) marker assays were designed on the single-nucleotide polymorphisms (SNPs) associated with the QTL significance peaks. Besides contributing to the development of pea genomic resources, this work lays the foundation for the obtainment of pea cultivars resistant to Oc and the identification of genes involved in resistance to parasitic Orobanchaceae.
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Affiliation(s)
- Chiara Delvento
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Arcieri
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Angelo Raffaele Marcotrigiano
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Marzia Guerriero
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Valentina Fanelli
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Maria Dellino
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Pasquale Luca Curci
- Institute of Biosciences and Bioresources, National Research Council (CNR), Bari, Italy
| | - Harro Bouwmeester
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Concetta Lotti
- Department of Agricultural, Food and Environmental Sciences, University of Foggia, Foggia, Italy
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Stefano Pavan
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
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Ma H, Song Y, Zhang Y, Guo H, Lv G, Chen H, Liu J, Liu X, An Z, Wang L, Xu Q, Jiao C, Chen P. Critical Sites of Serine Acetyltransferase in Lathyrus sativus L. Affecting Its Enzymatic Activities. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7858-7865. [PMID: 37163296 DOI: 10.1021/acs.jafc.3c00678] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
LsSAT2 (serine acetyltransferase in Lathyrus sativus) is the rate-limiting enzyme in biosynthesis of β-N-oxalyl-l-α,β-diaminopropionic acid (β-ODAP), a neuroactive metabolite distributed widely in several plant species including Panax notoginseng, Panax ginseng, and L. sativus. The enzymatic activity of LsSAT2 is post-translationally regulated by its involvement in the cysteine regulatory complex in mitochondria via interaction with β-CAS (β-cyanoalanine synthase). In this study, the binding sites of LsSAT2 with the substrate Ser were first determined as Glu290, Arg316, and His317 and the catalytic sites were determined as Asp267, Asp281, and His282 via site-directed/truncated mutagenesis, in vitro enzymatic activity assay, and functional complementation of the SAT-deficient Escherichia coli strain JM39. Furthermore, the C-terminal 10-residue peptide of LsSAT2 is confirmed to be critical to interact with LsCAS, and Ile336 in C10 peptide is the critical amino acid. These results will enhance our understanding of the regulation of LsSAT2 activities and the biosynthesis of β-ODAP in L. sativus.
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Affiliation(s)
- Hao Ma
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yaoyao Song
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huiying Guo
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Guowen Lv
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hong Chen
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiayi Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoning Liu
- School of Medicine, Huanghe S&T University, Zhengzhou, Henan 450063, China
| | - Zhenfeng An
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lei Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Quanle Xu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chengjin Jiao
- College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, Gansu 741000, China
| | - Peng Chen
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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Rispail N, Wohor OZ, Osuna-Caballero S, Barilli E, Rubiales D. Genetic Diversity and Population Structure of a Wide Pisum spp. Core Collection. Int J Mol Sci 2023; 24:2470. [PMID: 36768792 PMCID: PMC9916889 DOI: 10.3390/ijms24032470] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Peas (Pisum sativum) are the fourth most cultivated pulses worldwide and a critical source of protein in animal feed and human food. Developing pea core collections improves our understanding of pea evolution and may ease the exploitation of their genetic diversity in breeding programs. We carefully selected a highly diverse pea core collection of 325 accessions and established their genetic diversity and population structure. DArTSeq genotyping provided 35,790 polymorphic DArTseq markers, of which 24,279 were SilicoDArT and 11,511 SNP markers. More than 90% of these markers mapped onto the pea reference genome, with an average of 2787 SilicoDArT and 1644 SNP markers per chromosome, and an average LD50 distance of 0.48 and 1.38 Mbp, respectively. The pea core collection clustered in three or six subpopulations depending on the pea subspecies. Many admixed accessions were also detected, confirming the frequent genetic exchange between populations. Our results support the classification of Pisum genus into two species, P. fulvum and P. sativum (including subsp. sativum, arvense, elatius, humile, jomardii and abyssinicum). In addition, the study showed that wild alleles were incorporated into the cultivated pea through the intermediate P. sativum subsp. jomardii and P. sativum subsp. arvense during pea domestication, which have important implications for breeding programs. The high genetic diversity found in the collection and the high marker coverage are also expected to improve trait discovery and the efficient implementation of advanced breeding approaches.
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Affiliation(s)
- Nicolas Rispail
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Osman Zakaria Wohor
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Savanna Agriculture Research Institute, CSIR, Nyankpala, Tamale P.O. Box TL52, Ghana
| | | | - Eleonora Barilli
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Diego Rubiales
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
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Shi B, Haq IU, Fiaz S, Alharthi B, Xu ML, Wang JL, Hou WH, Feng XB. Genome-wide identification and expression analysis of the ZF-HD gene family in pea ( Pisum sativum L.). Front Genet 2023; 13:1089375. [PMID: 36685917 PMCID: PMC9849798 DOI: 10.3389/fgene.2022.1089375] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Pea is a conventional grain-feed-grass crop in Tibet and the only high-protein legume in the region; therefore, it plays an important role in Tibetan food and grass security. Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes, which play an important role in plant growth, development, and response to adversity stress. Using a bioinformatics approach, 18 PsZF-HD family members were identified. These genes were distributed across seven chromosomes and two scaffold fragments, and evolutionary analysis classified them into two subgroups, MIF and ZHD. The MIF subgroup was subdivided into three subclasses (PsMIFⅠ-III), and the ZHD subgroup was subdivided into five subclasses (ZHDⅠ-V). The PsZF-HD members were named PsMIF1-PsMIF4 and PsZHD1-PsZHD14. Twelve conserved motifs and four conserved domains were identified from PsZF-HD family, of which MIF subgroup only contained one domain, while ZHD subgroup contained two types of domains. In addition, there were significant differences in the three-dimensional structures of the protein members of the two subgroups. Most PsZF-HD genes had no introns (13/18), and only five genes had one intron. Forty-five cis-acting elements were predicted and screened, involving four categories: light response, stress, hormone, and growth and development. Transcriptome analysis of different tissues during pea growth and development showed that PsZHD11, 8, 13, 14 and MIF4 were not expressed or were individually expressed in low amounts in the tissues, while the other 13 PsZF-HDs genes were differentially expressed and showed tissue preference, as seen in aboveground reproductive organs, where PsZHD6, 2, 10 and MIF1 (except immature seeds) were highly expressed. In the aerial vegetative organs, PsZHD6, 1, and 10 were significantly overexpressed, while in the underground root system, PsMIF3 was specifically overexpressed. The leaf transcriptome under a low-nitrogen environment showed that the expression levels of 17 PsZF-HDs members were upregulated in shoot organs. The leaf transcriptome analysis under a low-temperature environment showed stress-induced upregulation of PsZHD10 and one genes and down-regulation of PsZHD6 gene. These results laid the foundation for deeper exploration of the functions of the PsZF-HD genes and also improved the reference for molecular breeding for stress resistance in peas.
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Affiliation(s)
- Bowen Shi
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China
| | - Inzamam Ul Haq
- College of Plant Protection, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Badr Alharthi
- Department of Biology, University College of Al Khurmah, Taif University, Saudi Arabia
| | - Ming-Long Xu
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China
| | - Jian-Lin Wang
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China
| | - Wei-Hai Hou
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China,*Correspondence: Wei-Hai Hou, ; Xi-Bo Feng,
| | - Xi-Bo Feng
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China,*Correspondence: Wei-Hai Hou, ; Xi-Bo Feng,
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Li X, Ma L, Wang Y, Ye C, Guo C, Li Y, Mei X, Du F, Huang H. PlantNLRatlas: a comprehensive dataset of full- and partial-length NLR resistance genes across 100 chromosome-level plant genomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1178069. [PMID: 37123823 PMCID: PMC10146310 DOI: 10.3389/fpls.2023.1178069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
Plants have evolved two layers of protection against biotic stress: PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI). The primary mechanism of ETI involves nucleotide-binding leucine-rich repeat immune receptors (NLRs). Although NLR genes have been studied in several plant species, a comprehensive database of NLRs across a diverse array of species is still lacking. Here, we present a thorough analysis of NLR genes across 100 high-quality plant genomes (PlantNLRatlas). The PlantNLRatlas includes a total of 68,452 NLRs, of which 3,689 are full-length and 64,763 are partial-length NLRs. The majority of NLR groups were phyletically clustered. In addition, the domain sequences were found to be highly conserved within each NLR group. Our PlantNLRatlas dataset is complementary to RefPlantNLR, a collection of NLR genes which have been experimentally confirmed. The PlantNLRatlas should prove helpful for comparative investigations of NLRs across a range of plant groups, including understudied taxa. Finally, the PlantNLRatlas resource is intended to help the field move past a monolithic understanding of NLR structure and function.
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Affiliation(s)
- Xiang Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Linna Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Yingmin Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Chen Ye
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Cunwu Guo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Yingbin Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Xinyue Mei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Fei Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
- *Correspondence: Huichuan Huang,
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Jha UC, Nayyar H, von Wettberg EJB, Naik YD, Thudi M, Siddique KHM. Legume Pangenome: Status and Scope for Crop Improvement. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223041. [PMID: 36432770 PMCID: PMC9696634 DOI: 10.3390/plants11223041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 05/31/2023]
Abstract
In the last decade, legume genomics research has seen a paradigm shift due to advances in genome sequencing technologies, assembly algorithms, and computational genomics that enabled the construction of high-quality reference genome assemblies of major legume crops. These advances have certainly facilitated the identification of novel genetic variants underlying the traits of agronomic importance in many legume crops. Furthermore, these robust sequencing technologies have allowed us to study structural variations across the whole genome in multiple individuals and at the species level using 'pangenome analysis.' This review updates the progress of constructing pangenome assemblies for various legume crops and discusses the prospects for these pangenomes and how to harness the information to improve various traits of economic importance through molecular breeding to increase genetic gain in legumes and tackle the increasing global food crisis.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research, Kanpur 208024, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Eric J. B. von Wettberg
- Department and Plant and Soil Science, Gund Institute for the Environment, The University of Vermont, Burlington, VT 05405, USA
| | - Yogesh Dashrath Naik
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa 848125, India
| | - Mahendar Thudi
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa 848125, India
- Shandong Academy of Agricultural Sciences, Jinan 250100, China
- Department of Agricultural Biotechnology and Molecular Biology, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
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Wang X, Zhang J, Zhang J, Zhou C, Han L. Genome-wide characterization of AINTEGUMENTA-LIKE family in Medicago truncatula reveals the significant roles of AINTEGUMENTAs in leaf growth. FRONTIERS IN PLANT SCIENCE 2022; 13:1050462. [PMID: 36407624 PMCID: PMC9669440 DOI: 10.3389/fpls.2022.1050462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
AINTEGUMENTA-LIKE (AIL) transcription factors are widely studied and play crucial roles in plant growth and development. However, the functions of the AIL family in legume species are largely unknown. In this study, 11 MtAIL genes were identified in the model legume Medicago truncatula, of which four of them are MtANTs. In situ analysis showed that MtANT1 was highly expressed in the shoot apical meristem (SAM) and leaf primordium. Characterization of mtant1 mtant2 mtant3 mtant4 quadruple mutants and MtANT1-overexpressing plants revealed that MtANTs were not only necessary but also sufficient for the regulation of leaf size, and indicated that they mainly function in the regulation of cell proliferation during secondary morphogenesis of leaves in M. truncatula. This study systematically analyzed the MtAIL family at the genome-wide level and revealed the functions of MtANTs in leaf growth. Thus, these genes may provide a potential application for promoting the biomass of legume forages.
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